Algodoo

This works much better for molecular simulation then the ones suppose to simulate this stuff in my saves. How does it work?

Link to my save regarding this stuff (im useing in-built browser so i cant just edit sadly) http://www.algodoo.com/algobox/details.php?id=125041

Basically it uses attraction, the green ones have none, the red ones have 100 attraction, and the blue ones have -100, it really just shows how atoms want to fuse and break at the same time. If you want, i can try and add the element of quarks.
Also:
The red ones can't collide with each other, same with the blue ones.
The green ones act as "glue" and are attracted by both.
And when the green ones decay, the red and blue ones will go into very small clusters, making them get blown up constantly by their own attraction.
.
You understand now?

You actually made some thing like this. Link is here.